I just noticed that KanR and NeoR used in bacterial selection and mammalian selection are related if not identical. I didn't consider when cloning a puro resistance casette into pCR4 TOPO (which carries the Kanamycin promoter driving KanR gene for bacterial selection). I worry that the KanR gene would be somehow (maybe leakily) expressed from the vector in mammalian cells and it will make that mammalian cells also NeoR (which is undesirable as I only intend to make the transfected cells puro resistance) if transfected with that plasmid. Please help!

as long as you have no eukaryotic promoter upstream of your kanamycin/neomycin (whatever) you don't have to worry ...the kan/neo is often driven by the SV40 (like in pcDNA3.1) ...so watch out for this one.